ARUP Journal Article Publications Archive

The Institute for Clinical and Experimental Research® is focused on the development of new diagnostic assays in a wide range of disciplines. Researchers at the institute regularly publish in respected, peer-reviewed journals, give presentations at national and international organizations, author books and book chapters, and develop new tests.

Publications by Year

Recent Publications

Mathison BA, Couturier MR, Pritt BS. Diagnostic Identification and Differentiation of Microfilariae. Journal of Clinical Microbiology. 57:e00706-19.

Lau AF, Walchak RC, Miller HB, Slechta ES, KAMBOJ K, Riebe K, Robertson AE, Gilbreath JJ, Mitchell KF, Wallace MA, Bryson AL, Balada-Llasat J, Bulman A, Buchan BW, Burnham CD, Butler-Wu S, Desai U, Doern CD, Hanson KE, Henderson CM, Kostrzewa M, Ledeboer NA, Maier T, Pancholi P, Schuetz AN, Shi G, Wengenack NL, Zhang SX, Zelazny AM, Frank KM. Multicenter Study Demonstrates Standardization Requirements for Mold Identification by MALDI-TOF MS​. Frontiers in Microbiology. 10:2098.

Luca Brunelli, Sabrina M. Jenkins, James M. Gudgeon2, Steven B. Bleyl, Christine E. Miller, Tatiana Tvrdik, Shale A. Dames, Betsy Ostrander, Josue A. F. Daboub, Brandon A. Zielinski, Erin K. Zinkhan, Hunter R. Underhill, Theodore Wilson, Joshua L. Bonkowsky, Christian C. Yost, Lorenzo D. Botto, Justin Jenkins, Theodore J. Pysher, Pinar Bayrak‐Toydemir, Rong MaoTargeted gene panel sequencing for the rapid diagnosis of acutely ill infants.  Molecular Genetics and Genomic Medicine  2019 Jul; 7(7): e00796. 

​Hunsaker JJH, Wyness SP, Needham LL, Genzen JR. Evaluation of L-index interference limits on Roche cobas c502 and c702 immunoturbidimetric assays using endogenously lipemic specimens and intralipid spiking. Clinical Biochemistry. 70:18-23. 

​Hunsaker JJH, Wyness SP, Needham LL, Genzen JR. Evaluation of L-index interference limits on Roche cobas c502 and c702 immunoturbidimetric assays using endogenously lipemic specimens and intralipid spiking. Clinical Biochemistry. 70:18-23. 

Chisholm KM, Mohlman J, Liew M, Termuhlen A, Cairo MS, Gross TG, Perkins SL, Miles RR. IRF4 translocation status in pediatric follicular and diffuse large B-cell lymphoma patients enrolled in Children's Oncology Group trials. Pediatric Blood & Cancer. 66(8):e27770.

Paulraj P, Diamond S, Razzaqi F, Ozeran D, Longhurst M, Andersen EF, Toydemir RM, Hong B. Pediatric acute myeloid leukemia with t(7;21)(p22;q22). Genes, Chromosomes & Caner. 58(8):551-557. 

Ravkov EV, Charlton CM, Barker AP, Hill H, Peterson LK, Slev P, Tebo A, Voelkerding KV, Wittwer CT, Heikal N, Delgado J, Lázár-Molnár E, Kumánovics A. Evaluation of Mass Cytometry in the Clinical Laboratory. Clinical Cytometry Part B. 96(4):266-274. 

Pavlov IY, Parker RL, Lázár-Molnár E, Strathmann FG, Delgado JC. Inductively coupled plasma mass spectrometry assay for quantification of free infliximab in serum. Journal of Immunological Methods. 470:33-39.  

Mathison BA. [author/coauthor for: Anisakiasis, Ascariasis, Balantiosis, Capillariasis, Cryptosporidiosis, Cyclosporiasis, Echinococcosis, Enterobiasis, Fascioliasis, Fasciolopsiasis, Filariasis, Giardiasis, Liver Fluke Disease, Loiasis, Onchocerciasis, Pediculosis and Pthiriasis, Scabies, Tapeworm, Trichuriasis]. Control of Communicable Diseases: Laboratory Practice. ​Mathison BA. Loiasis. Pathology Outlines. Online.

Yoo JH, Brady SW, Acosta-Alvarez L, Rogers A, Peng J, Sorensen LK, Wolff RK, Mleynek T, Shin D, Rich CP, Kircher DA, Bild A, Odelberg SJ, Li DY, Holmen SL, Grossmann AH. The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State.​ Cancer Research. 79(11):2892-2908.

Margraf RL, VanSant-Webb C, Mao R, Viskochil DH, Carey J, Hanson H, D'Astous J, Grossmann A, Stevenson DA. NF1 somatic mutation in dystrophic scoliosis. Journal of Molecular Neuroscience. 68(1):11-18.

Ruiz-Llorente L, Chiapparino E, Plumitallo S, Danesino C, Bayrak-Toydemir P, Pagella F, Manfredi G, Bernabeu C, Jovine L, Olivieri C. Characterization of a mutation in the zona pellucida module of Endoglin that causes hereditary hemorrhagic telangiectasia. Gene. 696:33-39.

​Rets A, Clayton AL, Christensen RD, Agarwal AM. Molecular diagnostic update in hereditary hemolytic anemia and neonatal hyperbilirubinemia. International Journal of Laboratory Hematology. 41 Suppl 1:95-101.

​Williams M, Lidke DS, Hartmann K, George TI. PD-L1 Expression in Mastocytosis. International Journal of Molecular Sciences. 20(9).

​Smock KJ, Moser KA. What have we learned from coagulation laboratory participation in external quality programs? International Journal of Laboratory Hematology. 41 Suppl 1:49-55.

​Ruiz-Llorente L, McDonald J,Wooderchak-Donahue W, Briggs E, Chesnutt M,Bayrak-Toydemir P,Bernabeu C.Characterization of a family mutation in the 5' untranslated region of the endoglin gene causative of Hereditary Hemorrhagic Telangiectasia. Journal of Human Genetics.64(4):333-339.

​Hale AJ,Mathison B, Pritt BS, Collins K.Endemic Visceral Bot Fly Larvae Infection in Northern New York State. ID Cases.16:e00531.

​Van Cott EM,Smock KJ, Lippi G.Innovations in Thrombosis and Hemostasis: A Glimpse Towards the Future of Diagnostic Analyzers. Seminars in Thrombosis and Hemostasis.45(3):225-227.

​Purswani P, Meehan CA, Kuehn HS, Chang Y, Dasso JF, Meyer AK, Ujhazi B, Csomos K, Lindsay D, Alberdi T, Joychan S, Trotter J, Duff C, Ellison M, Bleesing J,Kumanovics A, Comeau AM, Hale JE, Notarangelo LD, Torgersen TR, Ochs HD, Sriaroon P, Oshrine B, Petrovic A, Rosenzweig SD, Leiding JW, Walter JE.Two Unique Cases of X-linked SCID: A Diagnostic Challenge in the Era of Newborn Screening. Frontiers in Pediatrics.7:55.

​De Biase I, Pasquali M, Asamoah A.Unusual Metabolites in Patient with Isovaleric Acidemia​.Clinical Chemistry.65(4):595-597.

Pyne MT, Tardif KD, Allen A, Sexsmith C, Lesher L, Adelman M, Janát-Amsbury MM, Schlaberg R.Clinical Performance of SurePath™ Preservative Compared to PreservCyt® with Cobas® and Hybrid Capture® 2 HPV Tests in a Colposcopy Population. Clinical Laboratory. 65(03/2019).

​Adl SM, Mathison BATaxonomy and Classification of Human Eukaryotic Parasites. Manual of Clinical Microbiology, Twelfth Edition. 2:2379-2388.

Talford III SR, Mathison BA. Arthropods of Medical Importance. Manual of Clinical Microbiology, Twelfth Edition. 2:2620-2641.

Mathison BA, Pritt BS. Medical Parasitology Taxonomy Update: 2016-2017. Journal of Clinical Microbiology. 57(2):e01067-18.

​Couturier MR, Mathison BA.Parasite Diagnostics​. . AACC Learning Lab for Laboratory Medicine on NEJM Knowledge+. Online.

​Bianchi P, Elisa Fermo E, Glader B, Kanno H,Agarwal A, Barcellini W, Eber S, Hoyer JD, Kuter DJ, Maia TM, Del Mar Mañu-Pereira M, Kalfa TA, Pissard S, Segovia JC, van Beers E, Gallagher PG, Rees DC, van Wijk R. Addressing the diagnostic gaps in pyruvate kinase (PK)deficiency: Consensusrecommendations on the diagnosis of PK deficiency​.American Journal ofHematology.94(1):149-161.

​Wu F,Jensen TL, McMillin GA. ​​​​Detection of in utero cannabis exposure in umbilical cord tissue by a​
sensitive liquid chromatography-tandem mass spectrometry method
Methods in Molecular Biology.1872:211-222.

​​Shen W,Szankasi P, Durtschi J,Kelley TW, Xu X.Genome-Wide Copy Number Variation Detection Using​
NGS: Data Analysis and Interpretation. Methods in Molecular Biology. 1908:113-124.

Rule GS, Rockwood AL, Johnson-Davis KL. ​LC-MS/MS Method for the Quantification of the Leflunomide Metabolite, Teriflunomide, in Human Serum/Plasma​. Methods in Molecular Biology. 1872:75-83.

​Merrigan S, Johnson-Davis KL.Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) Method to Quantify Gabapentin and Pregabalin in Urine.Methods in Molecular Biology. 1872:119-127.

Needham LL, Smy L, Lee MA, Kunzler TM,Genzen JR.Phlebotomy Tube Interference with Nuclear Magnetic Resonance (NMR) Lipoprotein Subclass Analysis.Clinica Chimica Acta. 488:235-24.

​Stenehjem DD, Hahn AW, Gill DM, Albertson D, Gowrishankar B, Merriman J,Agarwal AM, Thodima V, Harrington EB, Au TH, Maughan BL, Houldsworth J, Pal SK, Agarwal N.Predictive genomic markers of response to VEGF targeted therapy in metastatic renal cell carcinoma​. PLoS One. 14(1):e0210415.

​Wabuyele SL, McMillin GA.Quantitation of Ethyl beta-D-glucuronide in Human Umbilical Cord Tissue by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS)​.Methods in Molecular Biology. 1872:223-236.

Khan J, Schmidt RL, Spittal MJ,Smock KJ, Greene DN.Venous thrombotic risk in transgender women undergoing estrogen therapy: A systematic review and meta-analysis.Clinical Chemistry.65(1):57-66.

Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G,Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genetics.228-229:197-217.

​Wooderchak-Donahue WL, McDonald J, Farrell A, Akay G, Velinder M, Johnson P, VanSant-Webb C,Margraf R, Briggs E,Whitehead KJ, Thomson J, Lin AE, Pyeritz RE, Marth G,Bayrak-Toydemir P. Genome sequencing reveals a deep intronic splicing ACVRL1 mutation hotspot in Hereditary Haemorrhagic Telangiectasia. Journal of Medical Genetics.55(12):824-830.

​Delgado JC, Lázár-Molnár E. HLA in Transplantation and Beyond. Clinics in Laboratory Medicine​.38(4):xi-xii.

​Mathison BA, Couturier MC.Human Dirofilariasis.ASCP Case Reports.1-16.

​Profaizer T, Kumánovics A. Human Leukocyte Antigen Typing by Next-GenerationSequencing Clinics in Laboratory Medicine. 38(4):565-578.

​Kushnir M, Peterson L, Strathmann F. Parathyroid hormone related protein concentration in human serum and CSF correlates with age. Medicine Innovates.

​Lázár-Molnár E, Snyder M. The Role of Human Leukocyte Antigen in Celiac Disease Diagnostics​. Clinics in Laboratory Medicine.38(4):655-668.

​Liew M, Rowe LR, Szankasi P, Paxton CN, Kelley T, Toydemir RM, Salama ME. Characterizing atypical BCL6 signal patterns detected by digital fluorescence in situ hybridization (FISH) analysis. Annals of Laboratory Medicine.38(6):619-622.

​Rivera-Muñoz EA, Milko LV, Harrison SM, Azzariti DR, Kurtz CL, Lee K, Mester JL, Weaver MA, Currey E, Craigen W, Eng C, Funke B, Hegde M, Hershberger RE,Mao R, Steiner RD, Vincent LM, Martin CL, Plon SE, Ramos E, Rehm HL, Watson M, Berg JS. ClinGen Variant Curation Expert Panel experiences and standardized processes for disease and gene-level specification of the ACMG/AMP guidelines for sequence variant interpretation. Human Mutation.39(11):1614-1622.

​Hiemenz MC, Ostrow DG, Busse TM, Buckley J, Maglinte DT, Bootwalla M, Done J, Ji J, Raca G, Ryutov A,Xu X, Zhen CJ, Conroy JM, Hazard FK, Deignan JL, Rogers B, Treece AL, Parham DM, Gai X, Judkins AR, Triche TJ, Biegel JA. OncoKidsSM: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies. The Journal of Molecular Diagnostics.20(6):765-776.

​Harrison SM, Dolinksy JS, Chen W, Collins CD, Das S, Deignan JL, Garber KB, Garcia J, Jarinova O, Knight Johnson AE, Koskenvuo JW, Lee H,Mao R, Mar-Heyming R, McFaddin AS, Moyer K, Nagan N, Rentas S, Santani AB, Seppälä EH, Shirts BH, Tidwell T, Topper S, Vincent LM, Vinette K, Rehm HL; ClinGen Sequence Variant Inter-Laboratory Discrepancy Resolution Working Group.Scaling resolution of variant classification differences in ClinVar between 41 clinical laboratories through an outlier approach. Human Mutation.39(11):1641-1649.

​ Smith KA, Merrigan SD, Johnson-Davis KL. Selecting a Structural Analog as an Internal Standard for the Quantification of 6-MethylmercaptopurineLC-MS/MS. The Journal of Applied Laboratory Medicine.3(3):384-396.​

​Miller HK, Binder AM, Peterson A, Theel ES, Volpe JM,Couturier MR, Cherry CC, Kersh GJ. Trends in Q fever serologic testing by immunofluorescence from four large reference laboratories in the United States, 2012-2016.Scientific Reports.8(1):16670.

​Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U,Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ,Mao R; ClinGen Inborn Errors of Metabolism Working Group. Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene​. Human Mutation.39(11):1569-1580.

Schlaberg R, Barrett A, Edes K, Graves M, Paul L, Rychert J, Lopansri BK, Leung DT. Fecal host transcriptomics for non-invasive human mucosal immune profiling: proof of concept in clostridium difficile infection.​Pathogens & Immunity. 3(2):164-180.

Mollaoglu G, Jones A, Wait SJ, Mukhopadhyay A, Jeong S, Arya R, Camolotto SA, Mosbruger TL, Stubben CJ, Conley CJ, Bhutkar A, Vahrenkamp JM, Berrett KC, Cessna MH, Lane TE, Witt BL, Salama ME, Gertz J, Jones KB, Snyder EL, Oliver TG. The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment. Immunity.​49(4):764-779.e9.

Timbrook TT, Spivak ES, Hanson KE. Current and Future Opportunities for Rapid Diagnostics in Antimicrobial Stewardship.​The Medical Clinics of North America.102(5):899-911.

Lu J, Genzen JR, Grenache DG. Development of an enzymatic assay to measure lactate in perchloric acid-precipitated cerebrospinal fluid.​Clinica Chimica Acta.483:142-144.

La'ulu SL, Kalp KJ, Straseski JA. How Low Can You Go? Analytical Performance of Five Automated​ Testosterone Immunoassays. Clinical Biochemistry. 58:64-71.

Yuzyuk T, Lozier B, Schwarz EL, Viau K,Kish-Trier E, De Biase I. Intra-individual variability of long-chain fatty acids (C12-C24) in plasma and red blood cells. Prostaglandins, Leukotrienes and Essential Fatty Acids. 135 (2018) 30-38.

Spörndly-Neesa E, Boberg J, Ekstedt E, Holm L, Fakhrzadeh A, Dunderd L,Kushnir MM, Lejonklou MH, Lind M. Low-dose exposure to Bisphenol A during developmenthas limited effects on male​​reproductionin prepubertal and aging Fischer 344 rats.Reproductive Toxicology.81:196-206.

Vaughn CP, Costa JL, Feilotter HE, Petraroli R, Bagai V, Rachiglio AM, Marino FZ, Tops B, Kurth HM, Sakai K, Mafficini A, Bastien RRL, Reiman A, Le Corre D, Boag A, Crocker S, Bihl M, Hirschmann A, Scarpa A, Machado JC, Blons H, Sheils O, Bramlett K, Ligtenberg MJL, Cree IA, Normanno N, Nishio K, Laurent-Puig P​. Simultaneous Detection of Lung Fusions using a Multiplex RT-PCR Next Generation Sequencing-based Approach: A Multi-Institutional Research Study​. BMC Cancer​. 18(1):828.

Hellwig S, Nix DA,Gligorich KM, O'Shea JM, Thomas A, Fuertes CL, Bhetariya PJ, Marth GT,Bronner MP, Underhill HR.Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing​.PLoS One.13(7): e0197333. July 2018.

Johnson DN,Furtado LV, Long BC, Zhen CJ, Wurst M, Mujacic I, Kadri S, Segal JP, Antic T, Cipriani NA.Noninvasive Follicular Thyroid Neoplasms With Papillary-Like Nuclear Features (NIFTPs) Are Genetically and Biologically Similar to Adenomatous Nodules and Distinct From Papillary Thyroid Carcinomas With Extensive Follicular Growth.Archives of Pathology and Laboratory Medicine.142(7):838-850. July 2018.

Margraf RL, Durtschi J, Krock B, Newcomb TM, Bonkowsky J,Voelkerding KV, Bayrak-Toydemir P, Lutz RE, Swoboda KJ.Novel PLP1 Mutations Identified with Next-Generation Sequencing Expand the Spectrum of PLP1-Associated Leukodystrophy Clinical Phenotypes.Child Neurology Open.5:2329048X18789282. July 2018.

​​Schmidt RL, LoPresti J, McDermott MT MD, Zick SM,Straseski JA.DDoes Reverse Triiodothyronine Testing Have Clinical Utility? An Analysis of Practice Variation Based on Data from a National Reference Laboratory.Thyroid.28(7):842-848. July 2018.

​Tuttle KD, Krovi SH, Zhang J, Bedel R, Harmacek L,Peterson LK, Dragone LL, Lefferts A, Halluszczak C, Riemondy K, Hesselberth JR, Rao A, O'Connor BP, Marrack P, Scott-Browne J, Gapin L.TCR signal strength controls thymic differentiation of iNKT cell subsets.Nature Communications.9(1):2650. July 2018.

Body BA, Beard MA,Slechta ES, Hanson KE, Barker AP, Babady NE, McMillen T, Tang YW, Brown-Elliott BA, Iakhiaeva E, Vasireddy R, Vasireddy S, Smith T, Wallace RJ Jr, Turner S, Curtis L, Butler-Wu S, Rychert J.Evaluation of the Vitek MS v3.0 Matrix-Assisted Laser Desorption Ionization--Time of Flight Mass Spectrometry System for Identification of Mycobacterium and Nocardia species.Journal of Clinical Microbiology.Vol. 56, No. 6.

Philip B, Yu DX, Silvis MR, Shin CH, Robinson JP, Robinson GL, Welker AE, Angel SN, Tripp SR, Sonnen JA, VanBrocklin MW, Gibbons RJ, Looper RE, Colman H, Holmen SL. Mutant IDH1 Promotes Glioma Formation In Vivo. Cell Reports. 2018;23(5):1553-1564.

Wabuyele SL, Colby JM, McMillin GA. Detection of Drug-Exposed Newborns. Therapeutic Drug Monitoring. 40(2):166-185.

DeMille D, Carlston CM, Tam OH, Palumbos JC, Stalker HJ, Mao R, Zori RT, Viskochil DH, Park AH, Carey JC. Three novel GJB2 (connexin 26) variants associated with autosomal dominant syndromic and nonsyndromic hearing loss​. American Journal of Medical Genetics. Part A. 176(4):945-950.

Shen W, Paxton CN, Szankasi P, Longhurst M, Schumacher JA, Frizzell KA, Sorrells SM, Clayton AL, Jattani RP, Patel JL, Toydemir R, Kelley TW, Xu X.Detection of genome-wide copy number variants in myeloid malignancies using next-generation sequencing. Journal of Clinical Pathology. 71(4):372-378.

Erickson JA, Grenache DG. ​Performance Evaluation of a Serum S-100B ELISA for Use with Cerebrospinal Fluid.​ The Journal of Applied Laboratory Medicine. 2:811-813.

Foster CC, Lee AY, Furtado LV, Hart J, Alpert L, Xiao SY, Hyman NH, Sharma MR, Liauw S. Treatment outcomes and HPV characteristics for an institutional cohort of patients with anal cancer receiving concurrent chemotherapy and intensity-modulated radiation therapy. PLoS One. ;13(3):e0194234.

Kushnir MM, Peterson LK, Strathmann FG. Parathyroid Hormone Related Protein Concentration in Human Serum and CSF Correlates with Age. Clinical Biochemistry. 2018;52:56-60.

Christensen RD, Agarwal AM, Yaish HM, Reading NS, O'Brien EA, Prchal JT. Three Novel Spectrin Variants in Jaundiced Neonates. Clinical Pediatrics. 2018;57(1):19-26.

Frigeni M, Balakrishnan B, Yin X, Calderon FRO, Mao R, Pasquali M, Longo N. Functional and Molecular Studies in Primary Carnitine Deficiency. Human Mutation. 2017;38(12):1684-1699.

Qiang W, Antelope O, Zabriskie MS, Pomicter AD, Vellore NA, Szankasi P, Rea D, Cayuela JM, Kelley TW, Deininger MW, O'Hare T. Mechanisms of resistance to the BCR-ABL1 allosteric inhibitor asciminib. Leukemia. 2017;31(12):2844-2847.

Tolan NV, Horowitz GL, Graham CS, Hillyard D, Osburn W, Ray S. New Therapies for Treating Hepatitis C Virus: Impact on Laboratory Testing Recommendations and Clinical Management. Clinical Chemistry. 2017;63(12):1799-1805.

Tebo AE. Recent Approaches to Optimize Laboratory Assessment of Antinuclear Antibodies. Clinical and Vaccine Immunology.2017;24(12).